chr5-67166241-A-T

Variant names:

• chr5-67166241-A-T
• rs4699896
• NM_001164664.2:c.7062A>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001164664.2(MAST4):​c.7062A>T​(p.Thr2354Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T2354T) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MAST4 NM_001164664.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 8 publications found

Genes affected

MAST4 (HGNC:19037): (microtubule associated serine/threonine kinase family member 4) This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP7: Synonymous conserved (PhyloP=0.534 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164664.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	NM_001164664.2	MANE Select	c.7062A>T	p.Thr2354Thr	synonymous	Exon 29 of 29	NP_001158136.1
	MAST4	NM_001393524.1		c.7071A>T	p.Thr2357Thr	synonymous	Exon 30 of 30	NP_001380453.1
	MAST4	NM_001393525.1		c.6861A>T	p.Thr2287Thr	synonymous	Exon 28 of 28	NP_001380454.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	ENST00000403625.7	TSL:5 MANE Select	c.7062A>T	p.Thr2354Thr	synonymous	Exon 29 of 29	ENSP00000385727.1
	MAST4	ENST00000403666.5	TSL:1	c.6495A>T	p.Thr2165Thr	synonymous	Exon 28 of 28	ENSP00000384313.1
	MAST4	ENST00000443808.1	TSL:1	c.4230A>T	p.Thr1410Thr	synonymous	Exon 8 of 8	ENSP00000400551.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	5.7
DANN	Benign	0.84
PhyloP100		0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4699896; hg19: chr5-66462069;